Our goal is to define fundamental principles that govern regulation of transcription by 6S RNA and the biological consequences on cell growth and survival. The Escherichia coli 6S RNA is the prototype for small RNA regulation of transcription through direct interaction with RNA polymerase, although examples of this type of RNA-dependent regulation exist from humans to bacteria. 6S RNAs are conserved widely in diverse eubacteria, and our recent work in Bacillus subtilis revealed important and surprising differences in 6S RNA function between this diverse organism and E. coli, although it is clear that 6S RNAs in both organisms are key regulators of transcription critical for cell response to and survival of changing environmental conditions, particularly when nutrients are limiting. These results raise key questions about the global role of 6S RNAs in additional diverse bacteria. We propose to use an integrated approach that spans detailed interaction studies to broad physiological approaches to provide a global view of 6S RNA function. This proposal addresses three quite different levels of questions using a wide array of biochemical, genetic, and physiological approaches. First, we have demonstrated that E. coli 6S RNA is used by RNA polymerase to make an RNA product during recovery from starvation, and that this process is a key regulator of 6S RNA function.
Aim 1 proposes to generate a detailed model mapping 6S RNA-RNA polymerase interactions to provide insight into mechanisms of regulation. Detailed analysis takes advantage of differences between E. coli and B. subtilis RNA polymerase behaviors to uncover key questions.
Aim 2 takes a global approach to identify genes regulated by 6S RNAs in B. subtilis, which will provide important links between 6S RNA activity and the physiological consequences of regulation, undoubtedly contributing to our global understanding of general cell survival.
And Aim 3 sets out to characterize a structurally diverse 6S RNA from Rhodobacter sphaeroides with the goal of expanding our understanding of 6S RNA function, mechanisms of RNA polymerase regulation, and physiological relevance under diverse metabolisms.

Public Health Relevance

The goal of our work is to define fundamental principles that govern regulation of transcription by 6S RNA to elucidate its role in optimal cell survival in diverse organisms with different lifestyles and environmental niches. Basic understanding of transcription and gene expression, as well as the consequences for cell growth and survival, underlies essentially every aspect of the mission of NIH in human health, with important implications in normal development, in progression of diseases such as cancer, or for manipulation of the human microbiome to dissuade pathogenic and promote beneficial micro-organisms.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Prokaryotic Cell and Molecular Biology Study Section (PCMB)
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Sledjeski, Darren D
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University of Wisconsin Madison
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Chen, James; Wassarman, Karen M; Feng, Shili et al. (2017) 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase. Mol Cell 68:388-397.e6
Cavanagh, Amy T; Wassarman, Karen M (2014) 6S RNA, a global regulator of transcription in Escherichia coli, Bacillus subtilis, and beyond. Annu Rev Microbiol 68:45-60
Cabrera-Ostertag, Ignacio J; Cavanagh, Amy T; Wassarman, Karen M (2013) Initiating nucleotide identity determines efficiency of RNA synthesis from 6S RNA templates in Bacillus subtilis but not Escherichia coli. Nucleic Acids Res 41:7501-11
Cavanagh, Amy T; Wassarman, Karen M (2013) 6S-1 RNA function leads to a delay in sporulation in Bacillus subtilis. J Bacteriol 195:2079-86
Cavanagh, Amy T; Sperger, Jamie M; Wassarman, Karen M (2012) Regulation of 6S RNA by pRNA synthesis is required for efficient recovery from stationary phase in E. coli and B. subtilis. Nucleic Acids Res 40:2234-46
Storz, Gisela; Vogel, Jörg; Wassarman, Karen M (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43:880-91
Cavanagh, Amy T; Chandrangsu, Pete; Wassarman, Karen M (2010) 6S RNA regulation of relA alters ppGpp levels in early stationary phase. Microbiology 156:3791-800
Klocko, Andrew D; Wassarman, Karen M (2009) 6S RNA binding to Esigma(70) requires a positively charged surface of sigma(70) region 4.2. Mol Microbiol 73:152-64
Cavanagh, Amy T; Klocko, Andrew D; Liu, Xiaochun et al. (2008) Promoter specificity for 6S RNA regulation of transcription is determined by core promoter sequences and competition for region 4.2 of sigma70. Mol Microbiol 67:1242-56
Wassarman, Karen M (2007) 6S RNA: a regulator of transcription. Mol Microbiol 65:1425-31

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